but I`m fairly sure that weight didn`t equal thrust even at 1000'.
You are correct, and the text on the page has now been changed, see here:
http://www.vc10.net/History/Individual/XR809.html
As far as I know the reason for scrapping the aircraft was airframe damage, but I wouldn't be surprised if the original engine beam and engines themselves were not immediately available upon completion of the tests. They won't have gone missing. No-one would throw away two serviceable Conways just like that, they were probably used as spares by the RAF.